R: convertDMATRIX

convertDMATRIX {AlphaBeta}

R Documentation

convertDMATRIX

Description

calculate divergence times of the pedigree

Usage

convertDMATRIX(sample.info, branch.points, dmatrix, design)

Arguments

`sample.info`	input file containing information on generation times and pedigree lineages
`branch.points`	input file containing lineage branch points
`dmatrix`	input file containing 5mC divergence values for each sample pair
`design`	"sibling" or "direct"

Value

pedigree

Examples

## Get some toy data
file1 <- system.file("extdata/dm/","sampleInfo.csv", package="AlphaBeta")
file2<-system.file("extdata/dm/","branchPoints.csv", package="AlphaBeta")
file3<-system.file("extdata/dm/","AB-dMatrix-CG-0.99.csv", package="AlphaBeta")
sample.info <-read.table(file1,sep="\t", header=TRUE, stringsAsFactors = FALSE)
branch.points <-read.table(file2,sep="\t", header=TRUE, stringsAsFactors = FALSE)
dmatrix <-read.table(file3,sep="\t", header=TRUE, stringsAsFactors = FALSE)
pedigree <- convertDMATRIX(sample.info=sample.info,
 branch.points=branch.points,dmatrix=dmatrix,design="sibling")
head(pedigree)

[Package AlphaBeta version 1.1.0 Index]